Evaluate gene sets by cell type-specific gene expression
Wei Sun
2024-07-04
Setup
Check enrichment of gene sets
Read in gene info and gene set assignments
file_tag = sprintf("%s_BL_%s", cell_type_name, graph_weight)
assayed_genes = scan(sprintf("output/gene_list_%s.txt", file_tag),
what = character(), sep="\n")
gene_sets = scan(sprintf("output/name_s_%s.txt", file_tag),
what = character(), sep="\n")
gene_sets = sapply(gene_sets, strsplit, USE.NAMES=FALSE, split=",")
n_genes = sapply(gene_sets, length)
names(n_genes) = NULL
summary(n_genes)## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 1.00 25.00 27.00 26.18 28.00 29.00## [1] 40## [1] 1 23 24 24 24 25 25 25 25 25 25 26 26 26 26 26 27 27 27 27 27 27 27 28 28
## [26] 28 28 28 28 28 28 28 28 28 29 29 29 29 29 29Find gene symbols using the alias2Symbol function from
limma.
a2s = rep(NA, length(assayed_genes))
for(i in 1:length(assayed_genes)){
gi = assayed_genes[i]
ai = alias2Symbol(gi)
if(length(ai) > 1){
print(gi)
print(ai)
}
a2s[i] = ai[1]
}## [1] "HIST1H2BC"
## [1] "H2BC5" "H2BC4"
## [1] "MPP6"
## [1] "MPHOSPH6" "PALS2"
## [1] "MARS"
## [1] "MARS1" "SLA2"
## [1] "SEPT2"
## [1] "SEPTIN6" "SEPTIN2"##
## FALSE TRUE
## 1951 49##
## FALSE TRUE <NA>
## 45 1906 49gene_info = data.table(sym_in_data = assayed_genes, sym_limma = a2s)
gene_info[sym_in_data != sym_limma,]## sym_in_data sym_limma
## 1: ADPRHL2 ADPRS
## 2: AES TLE5
## 3: C12orf45 NOPCHAP1
## 4: C3orf58 DIPK2A
## 5: C6orf99 LINC02901
## 6: CBWD2 ZNG1B
## 7: CXorf57 RADX
## 8: FAM102A EEIG1
## 9: FAM122C PABIR3
## 10: FAM153C FAM153CP
## 11: FAM160A2 FHIP1B
## 12: GRASP TAMALIN
## 13: H2AFX H2AX
## 14: HIST1H2AG H2AC11
## 15: HIST1H2BC H2BC5
## 16: HIST1H2BK H2BC12
## 17: HIST1H2BN H2BC15
## 18: HIST1H3A H3C1
## 19: HIST1H3H H3C10
## 20: HIST1H4C H4C3
## 21: HIST2H2BF H2BC18
## 22: LRMP IRAG2
## 23: MFSD14C MFSD14CP
## 24: MKL1 MRTFA
## 25: MPP6 MPHOSPH6
## 26: RNASEH1-AS1 RNASEH1-DT
## 27: SEPT6 SEPTIN6
## 28: SEPT9 SEPTIN9
## 29: TMEM161B-AS1 TMEM161B-DT
## 30: ARNTL BMAL1
## 31: C6orf106 ILRUN
## 32: C6orf203 MTRES1
## 33: FAM129A NIBAN1
## 34: FAM160B1 FHIP2A
## 35: FAM192A PSME3IP1
## 36: HEXDC HEXD
## 37: HIST1H1E H1-4
## 38: KIAA0100 BLTP2
## 39: KIAA1551 RESF1
## 40: LARS LARS1
## 41: MARS MARS1
## 42: PLA2G16 PLAAT3
## 43: SEPT2 SEPTIN6
## 44: SMIM37 MTLN
## 45: YARS YARS1
## sym_in_data sym_limmagene_info[, gene_symbol := sym_in_data]
gene_info[which(sym_in_data != sym_limma & (gene_symbol != "MT-CO2")),
gene_symbol := sym_limma]
dim(gene_info)## [1] 2000 3## sym_in_data sym_limma gene_symbol
## 1: ABCD3 ABCD3 ABCD3
## 2: ABCG1 ABCG1 ABCG1
## 3: ABHD5 ABHD5 ABHD5
## 4: ABI1 ABI1 ABI1
## 5: ABLIM1 ABLIM1 ABLIM1## t1
## 1 2
## 1998 1## sym_in_data sym_limma gene_symbol
## 1: SEPT6 SEPTIN6 SEPTIN6
## 2: SEPT2 SEPTIN6 SEPTIN6Read in cell type-specific expression data
Cell type specific gene expression were downloaded from protein atlas.
## [1] 1587110 4## Gene Gene name Cell type nTPM
## 1: ENSG00000000003 TSPAN6 Adipocytes 149.5
## 2: ENSG00000000003 TSPAN6 Alveolar cells type 1 6.1
## 3: ENSG00000000003 TSPAN6 Alveolar cells type 2 10.5
## 4: ENSG00000000003 TSPAN6 Astrocytes 13.9
## 5: ENSG00000000003 TSPAN6 B-cells 1.5## [1] 79##
## Adipocytes Alveolar cells type 1
## 20090 20090
## Alveolar cells type 2 Astrocytes
## 20090 20090
## B-cells Basal keratinocytes
## 20090 20090
## Basal prostatic cells Basal respiratory cells
## 20090 20090
## Basal squamous epithelial cells Bipolar cells
## 20090 20090
## Breast glandular cells Breast myoepithelial cells
## 20090 20090
## Cardiomyocytes Cholangiocytes
## 20090 20090
## Club cells Collecting duct cells
## 20090 20090
## Cone photoreceptor cells Cytotrophoblasts
## 20090 20090
## dendritic cells Distal enterocytes
## 20090 20090
## Distal tubular cells Ductal cells
## 20090 20090
## Early spermatids Endometrial ciliated cells
## 20090 20090
## Endometrial stromal cells Endothelial cells
## 20090 20090
## Enteroendocrine cells Erythroid cells
## 20090 20090
## Excitatory neurons Exocrine glandular cells
## 20090 20090
## Extravillous trophoblasts Fibroblasts
## 20090 20090
## Gastric mucus-secreting cells Glandular and luminal cells
## 20090 20090
## granulocytes Granulosa cells
## 20090 20090
## Hepatocytes Hofbauer cells
## 20090 20090
## Horizontal cells Inhibitory neurons
## 20090 20090
## Intestinal goblet cells Ionocytes
## 20090 20090
## Kupffer cells Langerhans cells
## 20090 20090
## Late spermatids Leydig cells
## 20090 20090
## Macrophages Melanocytes
## 20090 20090
## Microglial cells monocytes
## 20090 20090
## Mucus glandular cells Muller glia cells
## 20090 20090
## NK-cells Oligodendrocyte precursor cells
## 20090 20090
## Oligodendrocytes Pancreatic endocrine cells
## 20090 20090
## Paneth cells Peritubular cells
## 20090 20090
## Plasma cells Prostatic glandular cells
## 20090 20090
## Proximal enterocytes Proximal tubular cells
## 20090 20090
## Respiratory ciliated cells Rod photoreceptor cells
## 20090 20090
## Salivary duct cells Schwann cells
## 20090 20090
## Serous glandular cells Sertoli cells
## 20090 20090
## Skeletal myocytes Smooth muscle cells
## 20090 20090
## Spermatocytes Spermatogonia
## 20090 20090
## Squamous epithelial cells Suprabasal keratinocytes
## 20090 20090
## Syncytiotrophoblasts T-cells
## 20090 20090
## Theca cells Thymic epithelial cells
## 20090 20090
## Undifferentiated cells
## 20090## [1] 602700 5## Gene Gene name Immune cell TPM pTPM
## 1: ENSG00000000003 TSPAN6 basophil NA 1.2
## 2: ENSG00000000003 TSPAN6 Central memory CD8 T-cell NA 1.7
## 3: ENSG00000000003 TSPAN6 classical monocyte NA 0.2
## 4: ENSG00000000003 TSPAN6 Effector memory CD8 T-cell NA 0.7
## 5: ENSG00000000003 TSPAN6 Exhausted memory B-cell NA 0.7## Mode NA's
## logical 602700## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 0.00 0.00 3.10 49.74 27.20 96572.50## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 0.10 1.70 11.60 67.96 42.80 96572.50## [1] 30##
## basophil Central memory CD8 T-cell
## 20090 20090
## classical monocyte Effector memory CD8 T-cell
## 20090 20090
## Exhausted memory B-cell intermediate monocyte
## 20090 20090
## MAIT T-cell Memory CD4 T-cell TFH
## 20090 20090
## Memory CD4 T-cell Th1 Memory CD4 T-cell Th1/Th17
## 20090 20090
## Memory CD4 T-cell Th17 Memory CD4 T-cell Th2
## 20090 20090
## myeloid DC naive B-cell
## 20090 20090
## naive CD4 T-cell naive CD8 T-cell
## 20090 20090
## neutrophil NK-cell
## 20090 20090
## non-classical monocyte Non-switched memory B-cell
## 20090 20090
## Non-Vd2 gdTCR Plasmablast
## 20090 20090
## plasmacytoid DC Progenitor cell
## 20090 20090
## Switched memory B-cell T-reg
## 20090 20090
## Terminal effector memory CD4 T-cell Terminal effector memory CD8 T-cell
## 20090 20090
## total PBMC Vd2 gdTCR
## 20090 20090## [1] 30 2## Cell_type Lineage
## 1: Basophil Granulocytes
## 2: Neutrophil GranulocytesCheck gene expression for each gene set
## [1] 2000 3for(k in 1:length(gene_sets)){
if(length(gene_sets[[k]]) < 10) { next }
print(k)
set_k = paste0("set_", k)
print(gene_sets[[k]])
genes = gene_info[sym_in_data %in% gene_sets[[k]], gene_symbol]
n_genes = sum(genes %in% ct_immune$`Gene name`)
print(sprintf("found %d genes.", n_genes))
if(n_genes == 0) { next }
df = ct_immune[`Gene name` %in% genes,]
dim(df)
df[1:2,]
stopifnot(all(str_to_lower(df$`Immune cell`) %in%
str_to_lower(lineage$Cell_type)))
mat1 = match(str_to_lower(df$`Immune cell`),
str_to_lower(lineage$Cell_type))
df = cbind(df, lineage[mat1,])
df[1:2,]
df$Cell_type = factor(df$Cell_type, levels = lineage$Cell_type)
df = df[df$Lineage != "Total PBMC",]
df$Lineage = factor(df$Lineage,
levels = setdiff(lineage$Lineage, "Total PBMC"))
p1 = ggplot(df, aes(x=Cell_type, y=log10(pTPM + 0.1), fill=Lineage)) +
geom_boxplot() + xlab("Cell type") + ggtitle(set_k) +
theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
scale_fill_brewer(palette="RdBu")
print(p1)
}## [1] 1
## [1] "CCNH" "ERCC5" "LAX1" "POU2F2" "SENP7" "UTP6"
## [7] "ARHGAP10" "ARID5B" "DTX3L" "GBP1" "GBP3" "GBP5"
## [13] "GON4L" "IRF1" "IRF9" "MIER1" "MYO1F" "MYO1G"
## [19] "PARP14" "PARP9" "RHOH" "RNF19A" "SAMD9L" "SH3BP2"
## [25] "TGS1" "XAF1"
## [1] "found 26 genes."
## [1] 2
## [1] "CHD2" "ADGRE5" "ADGRG1" "AKNA" "CARD16"
## [6] "CCL4" "CD300A" "CTSW" "FCRL6" "FGFBP2"
## [11] "GPR65" "KIAA0040" "MESD" "MIR4435-2HG" "MYBL1"
## [16] "NAA38" "PAXX" "RASAL3" "S100A12" "S1PR5"
## [21] "SLFN12L" "TRANK1" "TRAV29DV5" "TRBV6-1" "TSPAN32"
## [26] "TTC38" "UBALD2" "ZNF683"
## [1] "found 26 genes."
## [1] 3
## [1] "ABHD5" "AL118516.1" "ATG13" "C16orf74" "CFAP36"
## [6] "CTSF" "EVI2B" "FAM118A" "FAM153C" "MAP3K8"
## [11] "MAST4" "NUAK2" "PARP8" "PNPLA2" "RGS1"
## [16] "RIC1" "SCML4" "SLC26A11" "SLC7A6" "SNRK"
## [21] "TBCC" "TCP11L2" "TMEM107" "ZFAND5" "ZMAT1"
## [26] "SCAMP4" "SDF2" "SP140"
## [1] "found 26 genes."
## [1] 4
## [1] "ADPRHL2" "ASAH1" "DHRS3" "FAM227B" "GPA33" "GPX4"
## [7] "HINT1" "HINT3" "HVCN1" "LTA4H" "MID1IP1" "OTUD5"
## [13] "PHC1" "PPIL3" "PTGER4" "RNF220" "RPL41" "SFMBT1"
## [19] "TAGLN2" "TRAV13-2" "TRAV9-2" "C12orf75" "FKBP2" "GSR"
## [25] "HEXDC" "LAP3" "TIMP1" "TMEM62"
## [1] "found 28 genes."
## [1] 5
## [1] "AC007952.4" "AC015982.1" "AC025164.1" "AC087239.1" "AC093323.1"
## [6] "AC245014.3" "ADA2" "AL133415.1" "AL138963.3" "ARL4A"
## [11] "COQ10A" "COQ8A" "FAM122C" "IL23A" "ILF3-DT"
## [16] "LETM2" "LRRC8C-DT" "MBNL2" "MLXIP" "NBPF14"
## [21] "PLCL1" "PRR7" "RABL2B" "RNASEK" "SNHG8"
## [26] "TBC1D7" "TRAV38-2DV8" "TSPOAP1-AS1" "PPP2R3C"
## [1] "found 17 genes."
## [1] 6
## [1] "AC087623.3" "ATG9B" "CD40LG" "COQ10B" "COQ7"
## [6] "CSKMT" "MAML2" "ODC1" "PDE7A" "RAB33B"
## [11] "SLC22A17" "SLC2A3" "SNHG12" "TAGAP" "TBCCD1"
## [16] "THAP6" "TRAV12-1" "TRAV41" "UBL3" "WHAMM"
## [21] "WSB1" "XIST" "ZC3H12D" "ZNF10" "ZNF831"
## [26] "CCDC43" "PPRC1" "ZNF267"
## [1] "found 25 genes."
## [1] 7
## [1] "CBR3" "CHMP4A" "CST3" "DNAAF2" "GGT7" "SLC25A32"
## [7] "TBPL1" "USP3" "B3GALT4" "CCDC112" "CTSC" "DOCK11"
## [13] "EFHD2" "FKBP11" "GNG2" "GZMB" "LPCAT4" "LRRFIP1"
## [19] "MATK" "NKG7" "PMVK" "PREX1" "PTGDR" "SACS"
## [25] "SH3BGRL3" "SMAP1" "SRGN"
## [1] "found 27 genes."
## [1] 8
## [1] "AMD1" "ARHGAP9" "C3orf58" "CCDC141" "CDC42SE2" "CHMP1B"
## [7] "FAM117B" "GRASP" "IER5" "IFRD1" "LBH" "MBD6"
## [13] "MTERF4" "MTRNR2L12" "MYNN" "RGCC" "TMC8" "TSC22D2"
## [19] "TSC22D3" "TTC31" "ADAM19" "CD69" "GCN1" "HIVEP3"
## [25] "MORC3" "STAT4" "TCF25" "ZEB2"
## [1] "found 28 genes."
## [1] 9
## [1] "CBLL1" "CD38" "CDC37L1" "DSE" "FCGR3A" "GIMAP8"
## [7] "LCP2" "SLC25A33" "SNX18" "TRBC2" "ZBTB25" "C4orf48"
## [13] "FAM129A" "GNG5" "GNPTAB" "HLA-DPA1" "LAG3" "NDUFA3"
## [19] "NRROS" "NUS1" "OAS2" "SLA" "SPOCK2" "SRP54"
## [25] "TRAT1" "UBR2"
## [1] "found 26 genes."
## [1] 10
## [1] "ARMCX5" "C17orf49" "CXorf57" "DBP" "FOXO1" "HIST1H3H"
## [7] "NEK1" "PEX6" "PHYH" "RNF113A" "SBF2" "YPEL2"
## [13] "ZSCAN18" "COLGALT1" "FNDC3B" "GCA" "GNPAT" "KHNYN"
## [19] "KIF21A" "KIF21B" "PEX26" "PHF23" "PLEKHA2" "RAPGEF1"
## [25] "TNFRSF18"
## [1] "found 25 genes."
## [1] 11
## [1] "ANAPC4" "ATF4" "EGR1" "EIF1" "EIF5" "EPHB6" "EPHX2"
## [8] "FOSB" "JUNB" "LYRM7" "MALAT1" "NDE1" "NEU1" "NUP54"
## [15] "PLCD1" "PNRC1" "SAT1" "SP3" "STK19" "TCF7" "TOB2"
## [22] "BHLHE40" "GPHN" "MAF" "SRFBP1" "TRAC"
## [1] "found 25 genes."
## [1] 12
## [1] "AP002360.1" "ARHGAP15" "C1GALT1" "CD27" "ERAP2"
## [6] "FCN1" "GIMAP1" "IGLV1-44" "IGLV2-14" "JPX"
## [11] "KCNK6" "KLF7" "LEPROT" "LRMP" "PCMTD2"
## [16] "PYROXD1" "RAB37" "SLC38A1" "STK17A" "TRBC1"
## [21] "TTC39C" "UCP2" "XRRA1" "ZNF84" "ZNF862"
## [26] "GZMA" "IFI44" "KLRG1"
## [1] "found 26 genes."
## [1] 13
## [1] "ADD3" "C1orf43" "CASP4" "CD48" "CD96" "EVL" "FOXN3"
## [8] "IL16" "IL27RA" "LETMD1" "SEPT6" "SFI1" "SH2D1A" "SLC12A7"
## [15] "STMN3" "TMEM204" "TRAM1" "TTC3" "ACAP3" "AZI2" "CLSTN1"
## [22] "JAKMIP1" "N4BP1" "SERTAD3" "UBA7"
## [1] "found 25 genes."
## [1] 14
## [1] "AKAP7" "BDH1" "CCR6" "CHMP7" "LCLAT1" "PDE3B"
## [7] "PPP1R15B" "RNF139" "SIMC1" "TMEM63A" "ALG11" "ATP8B2"
## [13] "BST2" "GGCX" "IFNGR2" "LPCAT3" "LPGAT1" "NPDC1"
## [19] "PIEZO1" "RAB8B" "TCIRG1" "TSPAN2" "ZDHHC20"
## [1] "found 23 genes."
## [1] 15
## [1] "ATAD1" "GZMK" "HDHD2" "IGKV3-20" "LRRC8D" "PECR"
## [7] "SLC25A25" "TOX" "TRAV12-2" "TRAV14DV4" "TRAV23DV6" "TRAV8-2"
## [13] "TRBV6-6" "ARHGEF3" "BUD23" "CFD" "CX3CR1" "LINC01871"
## [19] "NNT-AS1" "PCED1B" "PLP2" "PTGER2" "S100A11" "TM2D1"
## [25] "TMEM156" "TRBV12-3" "TTC16" "USP30-AS1"
## [1] "found 25 genes."
## [1] 16
## [1] "AGO3" "CDC25B" "CDK13" "DCTN4" "DENND4A" "DUSP2"
## [7] "FAM110A" "FAM160A2" "FAM53C" "GCH1" "MAP2K5" "MAP2K6"
## [13] "MAP3K2" "NOG" "NT5C2" "PPM1B" "RAP2C" "TMEM263"
## [19] "ZNF638" "DICER1" "GIGYF2" "KIF13B" "MAP4" "MAST3"
## [25] "RNF144A" "TMEM33"
## [1] "found 25 genes."
## [1] 17
## [1] "AC013264.1" "AC025159.1" "AC119396.1" "AC245297.3" "AK5"
## [6] "ANXA2R" "BOLA2-SMG1P6" "C12orf29" "DELE1" "GIMAP6"
## [11] "LINC00861" "LST1" "LYRM9" "MCUB" "OTULINL"
## [16] "POLD4" "SLC25A38" "SNHG7" "SPART" "TC2N"
## [21] "TMEM161B-AS1" "TRAV8-3" "TRBV28" "WAPL" "WASHC4"
## [26] "ZNF749" "C1orf162" "TUT4"
## [1] "found 21 genes."
## [1] 18
## [1] "C1orf174" "FLI1" "IRF2BP2" "OXLD1" "PAPOLG" "SS18"
## [7] "ZNF821" "ADAR" "AFF1" "ARHGAP4" "DEK" "DHX29"
## [13] "DIS3" "ETV6" "IFIT2" "IQSEC1" "KIF2A" "MLEC"
## [19] "MLLT10" "MLLT6" "POGLUT1" "PVT1" "ROMO1" "SECISBP2"
## [25] "SOCS2" "ZNF593"
## [1] "found 25 genes."
## [1] 19
## [1] "AC008105.3" "AC145124.1" "ADK" "DGKA" "MMP28"
## [6] "NT5DC1" "WARS2" "AC020915.3" "AC022916.1" "APOL1"
## [11] "BISPR" "ECPAS" "FRMD4B" "HELB" "ICE1"
## [16] "IGLV3-25" "MTRNR2L8" "MX2" "NCBP3" "PRMT2"
## [21] "RSAD2" "SESN3" "SETD5" "SP140L" "SPATA13"
## [26] "TCAF2" "TTTY15" "UTP25"
## [1] "found 22 genes."
## [1] 20
## [1] "ARID4A" "COG5" "DPEP2" "GATA3" "HEATR5B" "HELQ" "MTO1"
## [8] "MXD1" "NABP1" "PARP16" "PRKCH" "RASSF3" "SIKE1" "ST3GAL1"
## [15] "STX16" "ZNF490" "CCDC88C" "CHD6" "FRY" "FRYL" "FUT11"
## [22] "NBEAL2" "SLMAP" "TBX21" "ZBTB8OS"
## [1] "found 25 genes."
## [1] 21
## [1] "CSRNP1" "DAPP1" "EFCAB2" "IL6R" "KANSL2" "KDM6A" "MYLIP"
## [8] "NR1D1" "NR1D2" "TBCK" "TCTA" "ASCL2" "C12orf4" "CARD11"
## [15] "CREBZF" "KANSL1" "KMT2B" "KMT2C" "KMT2D" "NFE2L1" "PHF20"
## [22] "PHF20L1" "SCAF8" "UBE3B" "UTY"
## [1] "found 25 genes."
## [1] 22
## [1] "BTG1" "BTG2" "FBXL3" "FHIT" "INPP4B" "KIF9" "NR4A3"
## [8] "NSUN6" "RGS10" "SH3YL1" "TECPR1" "ACAP1" "ANKAR" "CCDC88B"
## [15] "CGGBP1" "CYTIP" "EFR3A" "ISG20" "KIF3B" "KLF6" "NARF"
## [22] "P4HTM" "PYCARD" "RECK" "TBC1D14" "TRAPPC8" "TSHZ2"
## [1] "found 27 genes."
## [1] 23
## [1] "BTN3A1" "CD28" "CD82" "MZF1" "PECAM1" "PITPNC1"
## [7] "PLK3" "PTPRCAP" "TMEM245" "TNFRSF25" "YPEL5" "APOBEC3G"
## [13] "BTN3A2" "CARD8-AS1" "CCL5" "CCR4" "CD2" "CD58"
## [19] "CST7" "GAB3" "GNLY" "ITGAL" "PLEK" "PTPRC"
## [25] "SMPD2" "SPON2" "TAOK3"
## [1] "found 26 genes."
## [1] 24
## [1] "IER3" "KLF10" "PLEKHM1" "AP3M2" "C1orf21" "COL6A3" "CRIP2"
## [8] "CRTC3" "DDX3Y" "EIF1AY" "ETNK1" "IL21R" "KDM5D" "LAIR2"
## [15] "LPIN1" "LPIN2" "NLRC5" "PIM1" "PPP2R5B" "RNF157" "RNPEPL1"
## [22] "RTKN2" "SBNO2" "SUSD6" "TAF4B" "TNFRSF4" "ZNF236"
## [1] "found 27 genes."
## [1] 25
## [1] "AC097376.2" "AL135791.1" "AL359220.1" "ARMH1" "CERNA1"
## [6] "CHRM3-AS2" "ERVK3-1" "IPCEF1" "JAML" "LINC00623"
## [11] "LINC01215" "LINC01550" "MATR3-1" "MHENCR" "MMP24OS"
## [16] "NPIPB5" "NSMCE3" "PITPNA-AS1" "RETREG1" "TRABD2A"
## [21] "TRAV21" "TRAV25" "TRBV5-4" "TRBV6-5" "ZFP14"
## [26] "ZNF506" "ZNF91" "PUS7L"
## [1] "found 17 genes."
## [1] 26
## [1] "ACADSB" "C12orf45" "CDKN2AIP" "FBXO8" "GSTM4" "GTPBP10"
## [7] "GTPBP6" "HIST1H2BC" "IP6K2" "METAP1" "NELFCD" "PHLDA1"
## [13] "ZNF7" "C2orf68" "CAMTA2" "GUF1" "HELZ2" "IGHMBP2"
## [19] "MTRF1L" "PDE12" "SUPV3L1" "TRMT10C" "ZNF483" "ZNF708"
## [1] "found 23 genes."
## [1] 27
## [1] "C6orf62" "CAMK4" "CCDC66" "CCM2" "CEP120" "CEP95" "CITED2"
## [8] "DPYD" "EPS8" "GADD45B" "HIVEP2" "HOXB2" "IER2" "KLF12"
## [15] "ODF2L" "PIK3IP1" "PNISR" "RCAN3" "RCSD1" "SLC44A1" "TESPA1"
## [22] "TGIF1" "ZFP36L1" "BLOC1S6" "IFI44L" "VPS36" "WDR7"
## [1] "found 27 genes."
## [1] 28
## [1] "ABCG1" "AC025171.2" "AC027644.3" "AC084033.3" "ARF4-AS1"
## [6] "ARRDC2" "GOLGA8B" "GPCPD1" "JCHAIN" "KCNQ1OT1"
## [11] "LINC00649" "LINC02265" "LINC02273" "MDS2" "MFSD14C"
## [16] "MUC20-OT1" "MZF1-AS1" "NAA16" "NDUFV2-AS1" "NOCT"
## [21] "NPIPB11" "RNASEH1-AS1" "ST7L" "THAP9-AS1" "TRAV8-6"
## [26] "TRBV7-3" "ZNF600" "AREG" "PKNOX1"
## [1] "found 14 genes."
## [1] 29
## [1] "AC009061.2" "ANKH" "CCNI" "COA1" "COX10"
## [6] "CRLF3" "DNASE1" "ENOSF1" "FCMR" "FYB1"
## [11] "IGKV1-5" "LIMD2" "LRRN3" "NUDT4" "ORC4"
## [16] "PCNP" "SLC8B1" "SPIDR" "STARD10" "TMEM154"
## [21] "TMEM71" "TRBV6-2" "TUBD1" "TUBE1" "YY1AP1"
## [26] "ZFAS1" "ZNF140" "SLC23A2" "TMEM175"
## [1] "found 27 genes."
## [1] 30
## [1] "ACSS1" "AIF1" "ATP5MG" "C7orf31" "DENND2D" "DUSP1"
## [7] "FAM102A" "HIST1H4C" "KLRB1" "LTB" "METTL21A" "NECAP2"
## [13] "NOP53" "RACK1" "RASA2" "RPL36A" "RPS26" "TIA1"
## [19] "TOMM7" "TSPYL1" "TSPYL2" "TSPYL4" "ZFX" "HSH2D"
## [25] "MX1" "NUP160" "OAS1"
## [1] "found 26 genes."
## [1] 31
## [1] "ABCC10" "ABHD2" "ABHD3" "AC116407.2" "AC118549.1"
## [6] "ADTRP" "ATAD2B" "C20orf204" "FAAH2" "GPR132"
## [11] "HACD3" "HRH2" "KANSL1-AS1" "LRRC58" "MFSD14A"
## [16] "NBDY" "NDUFC1" "NRDC" "OSM" "PARP11"
## [21] "PCSK1N" "PUM3" "SLF2" "THUMPD3-AS1" "TMEM138"
## [26] "TOMM70" "TSPAN14" "Z93930.2" "ZFYVE28"
## [1] "found 24 genes."
## [1] 32
## [1] "AC004687.1" "AC004854.2" "AC016405.3" "AC020911.2" "AC023157.3"
## [6] "AC025171.3" "AC083880.1" "AC091271.1" "AC103591.3" "AF213884.3"
## [11] "AL121944.1" "AL139246.5" "AL357060.1" "AL451085.1" "AL627171.1"
## [16] "AL645728.1" "ATP2B1-AS1" "BX284668.6" "C6orf99" "HIPK1-AS1"
## [21] "ID3" "KLHL6" "LINC01465" "NPIPB4" "NUP58"
## [26] "OSER1-DT" "SDR42E2" "Z93241.1" "SNHG9"
## [1] "found 5 genes."
## [1] 34
## [1] "ABTB1" "CHURC1" "CIRBP" "EIF3G" "EIF3K" "EIF3M"
## [7] "EIF4A2" "EPB41" "KLHL24" "LIMS1" "MAP4K2" "MARCKSL1"
## [13] "NMT2" "NOSIP" "POLL" "SCRN2" "SERTAD2" "UXT"
## [19] "WDR48" "DDX60" "PARVG" "RSU1" "TRIB2" "USP46"
## [1] "found 24 genes."
## [1] 35
## [1] "CD52" "COMMD6" "COMMD9" "CYB5D2" "FCGRT" "HLA-B"
## [7] "HLA-E" "HLA-F" "KIF20B" "SCPEP1" "SGSM3" "TNFAIP8"
## [13] "ZHX2" "B2M" "COMMD2" "DIAPH2" "EAPP" "EMB"
## [19] "G2E3" "HLA-DRB5" "MR1" "PRF1" "SHOC2" "ST6GAL1"
## [25] "TAPBP"
## [1] "found 25 genes."
## [1] 36
## [1] "CCNL1" "CENPK" "CLK4" "ITGB3BP" "NKTR" "PDCD7"
## [7] "PRPF38B" "RSRP1" "SMDT1" "ZNF677" "ZRSR2" "CLASRP"
## [13] "CWC25" "ERICH1" "IFI6" "KMT2E" "NKAP" "PARP4"
## [19] "PIP4K2B" "SAMD9" "SFSWAP" "SLTM" "SREK1IP1" "ZNF195"
## [1] "found 24 genes."
## [1] 37
## [1] "AKIRIN1" "AKIRIN2" "CD83" "CLDND1" "FAM8A1" "MYADM"
## [7] "OSER1" "ALOX5AP" "ATXN7L3B" "BROX" "CD320" "CD7"
## [13] "CDK2AP2" "DENND4B" "FBXO9" "LY96" "NT5C" "PSMB9"
## [19] "PSME2" "RNF145" "SDR39U1" "SELL" "SLC20A2" "TIPARP"
## [25] "UGCG"
## [1] "found 25 genes."
## [1] 38
## [1] "NSMAF" "TBC1D10C" "APH1B" "CISH" "CITED4" "CTBS"
## [7] "EHMT1" "GABPB2" "GMFB" "ICOS" "IFI35" "KCNAB2"
## [13] "KLF9" "LTBP3" "NADSYN1" "NEK9" "NME3" "PLAC8"
## [19] "PRDM2" "PREP" "REXO2" "SLC9A8" "STK10" "STK17B"
## [25] "TOB1" "ZNF101" "ZNF276"
## [1] "found 27 genes."
## [1] 39
## [1] "RBKS" "UPF3A" "AC016831.7" "AGAP2" "APBB1IP"
## [6] "ARL4C" "CARMIL2" "CD55" "CEMIP2" "CRYBG1"
## [11] "DDIT4" "GPRIN3" "GRK2" "IFITM2" "IRAK4"
## [16] "MIAT" "MT1X" "NFKBIZ" "NORAD" "NSD3"
## [21] "ODF3B" "PHPT1" "RAP1GAP2" "RPS4Y1" "SIGIRR"
## [26] "SLC25A37" "SMIM37" "TENT5C"
## [1] "found 25 genes."
## [1] 40
## [1] "APOL6" "BCL9L" "CMIP" "CROT" "EIF2AK4" "FAM53B"
## [7] "GIMAP4" "GIMAP7" "GZMM" "IL32" "KIAA1551" "KLHDC4"
## [13] "LY6E" "MCTP2" "MT2A" "NQO2" "PDE4B" "PEX11B"
## [19] "PLA2G16" "RCBTB2" "RNMT" "SEC14L1" "SH3BP5" "SYNE1"
## [25] "SYTL1" "TGFBR3" "VPS13D" "ZBP1" "ZNF292"
## [1] "found 29 genes."
Session information
## used (Mb) gc trigger (Mb) limit (Mb) max used (Mb)
## Ncells 4167295 222.6 11673970 623.5 NA 11673970 623.5
## Vcells 20576987 157.0 51369168 392.0 65536 51368243 392.0## R version 4.2.3 (2023-03-15)
## Platform: aarch64-apple-darwin20 (64-bit)
## Running under: macOS Ventura 13.4.1
##
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib
##
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] stringr_1.5.0 limma_3.54.2 tidyr_1.3.0 ggpubr_0.6.0
## [5] ggplot2_3.4.2 data.table_1.14.8
##
## loaded via a namespace (and not attached):
## [1] Rcpp_1.0.10 png_0.1-8 Biostrings_2.66.0
## [4] digest_0.6.31 utf8_1.2.3 R6_2.5.1
## [7] GenomeInfoDb_1.34.9 backports_1.4.1 stats4_4.2.3
## [10] RSQLite_2.3.1 evaluate_0.20 httr_1.4.6
## [13] pillar_1.9.0 zlibbioc_1.44.0 rlang_1.1.0
## [16] rstudioapi_0.14 car_3.1-2 jquerylib_0.1.4
## [19] blob_1.2.4 R.oo_1.25.0 R.utils_2.12.2
## [22] S4Vectors_0.36.2 rmarkdown_2.21 labeling_0.4.2
## [25] RCurl_1.98-1.12 bit_4.0.5 munsell_0.5.0
## [28] broom_1.0.4 compiler_4.2.3 xfun_0.39
## [31] pkgconfig_2.0.3 BiocGenerics_0.44.0 htmltools_0.5.5
## [34] tidyselect_1.2.0 KEGGREST_1.38.0 GenomeInfoDbData_1.2.9
## [37] tibble_3.2.1 IRanges_2.32.0 fansi_1.0.4
## [40] crayon_1.5.2 dplyr_1.1.2 withr_2.5.0
## [43] R.methodsS3_1.8.2 bitops_1.0-7 grid_4.2.3
## [46] jsonlite_1.8.4 gtable_0.3.3 lifecycle_1.0.3
## [49] DBI_1.1.3 magrittr_2.0.3 scales_1.2.1
## [52] cli_3.6.1 stringi_1.7.12 cachem_1.0.7
## [55] carData_3.0-5 farver_2.1.1 XVector_0.38.0
## [58] ggsignif_0.6.4 bslib_0.4.2 generics_0.1.3
## [61] vctrs_0.6.2 RColorBrewer_1.1-3 org.Hs.eg.db_3.16.0
## [64] tools_4.2.3 bit64_4.0.5 Biobase_2.58.0
## [67] glue_1.6.2 purrr_1.0.1 abind_1.4-5
## [70] fastmap_1.1.1 yaml_2.3.7 AnnotationDbi_1.60.2
## [73] colorspace_2.1-0 rstatix_0.7.2 memoise_2.0.1
## [76] knitr_1.44 sass_0.4.5